Add parameters to skip snv calling and repeat analysis #571
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jemten
approved these changes
Jun 24, 2024
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Nice to get it more coherent. I think it would be good to refactor the check for mandatory params in nf-core/raredisease. To me it would be preferable to spin that out to another subworkflow. Might be possible to do it here:
https://github.com/nf-core/raredisease/blob/dev/subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf
as it's done in gms/nallo:
https://github.com/genomic-medicine-sweden/nallo/blob/6fa3d442c20581a6bd718bbe09dfe8475a7d7974/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf#L168
separate PR though
workflows/raredisease.nf
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| if (!params.skip_repeat_analysis) { | ||
| if ( params.analysis_type.equals("wgs") ) { |
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Wouldn't it be better to write this in one if statement?
if (!params.skip_repeat_analysis && params.analysis_type.equals("wgs"))
| } | ||
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| if (!params.skip_snv_calling) { | ||
| mandatoryParams += ["genome"] |
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genome is also used by smncopynumbercaller, but maybe you're adding that in a later PR :)
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Yupe! I have a couple more PR's in line to be merged after this :D
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PR checklist
Adding two new parameters to make the workflows more modular. I did so we can skip certain workflows for specific analysis. For example, skip repeat calling for wes samples.
Also includes some minor refactoring to group related workflows together and make them more obvious in the main workflow.
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).